Talk:Bioinformatics tools
Protein to DNA code It looks like I have come across a bit of a problem. Not too long ago, I decided to look for a less ambiguous protein to DNA translator. I came across one that used chicken codons, and I decided to translate the dinosaur protein sequences using that instead. I quickly compared them with sequences translated using human codons and thought that they were the same. Now, I have decided to do it again, and it seems that I was wrong. After aligning the different codon results again, I found that the protein translations made using the chicken and the human codons were actually different by one base pair. I do not think this is too much of a problem, since humans and cows did seem to use the same codons and belonged to different superorders, but Brachylophosaurus and chickens differ even more. And I don't know how far removed a chicken is from T. rex. Do we have to use the ambiguous translator again? I personally don't want to, since they don't give precise results, but it seems that we might have to. Jurassic Park Treasury (talk) 09:21, June 3, 2013 (UTC) :This is my opinion. I think the bird code is our best shot for filling the caps. T. rex is clother related to birds than ANY other extant group. The common ancestor or chicken and Brachylophosaurus lived approximately 230 million years ago (first saurischian dinosaur). That is much later than its common ancestor with crocs or turtles. :However, I'm sure it wouldn't really matter for the cloning process. MismeretMonk (talk) 15:50, June 3, 2013 (UTC) Yeah, I should really stop worrying. I just compared the ambiguous nucleotides to the chicken codon nucleotides and they were pretty much the same. Jurassic Park Treasury (talk) 23:07, June 3, 2013 (UTC) I found this, which translates protein code into both ambiguous and non-ambiguous DNA code without using a specific codon. Would it be wiser to use this instead? Jurassic Park Treasury (talk) 09:05, July 30, 2013 (UTC) DNA or mRNA? I translated a hadrosaur actin protein sequence into a nucleotide sequence and decided to BLAST the latter. The results were good, but the problem was that the sequences it matched were not DNA sequences, but messenger RNA sequences. I know RNA is supposed to have A, G, C and U nucleotides, but all of the GenBank mRNA sequences use the T nucleotide, which is weird. Is it possible that the nucleotide translator I'm using creates RNA sequences? If so, we might need to go back to using the ambigious translator. Jurassic Park Treasury (talk) 10:07, July 25, 2013 (UTC) So, do you have anything to say about this? Jurassic Park Treasury (talk) 10:13, July 27, 2013 (UTC) :I don't know what to think of it right now. I've never used this stranslator. If you use the ambigious translator, do you get mRNA's in BLAST too? BastionMonk (talk) 12:22, July 27, 2013 (UTC) :No significant similarity was found when I BLASTed ambigious nucleotides. However, the ambigious code aligns perfectly with the non-ambigious code apart from the ambigious nucleotides. So I presume they would get the same results. Luckily, not all of the matches were mRNA. One of the matches was the DNA code for a fish actin gene, though it was only a 96% match, so it may not be time to panic just yet. The VAST majority of the list is still mRNA sequences though. We may need to consult a more experienced biologist about this. Jurassic Park Treasury (talk) 23:17, July 27, 2013 (UTC) :No need for all that. I used this translator to translate M''' into DNA code. It translates '''M into ATG. This is the code of the sense-DNA strand (and mRNA with U changed for T). (You know that DNA consists of 2 strands?) The code of the sense-DNA strand isn't the official code of the gene. The antisense-DNA strand was used to produce the mRNA, so the antisense-strand sequence is the official gene code. DNA is complementair. If the sense-strand reads ATGC, the antisense-strand reads TACG. :So, you either correct for this by hand or with software, or you will have to search a translator that translates the AA sequence into the antisense-DNA sequence. BastionMonk (talk) 14:00, July 28, 2013 (UTC) I found this program. When I submitted the ATGC sequence into it, it came out as TACG, so I think this is what we're looking for. Jurassic Park Treasury (talk) 22:06, July 28, 2013 (UTC) I BLASTed the antisense sequence for the actin gene. None of the matches were actin. Most of the matches were complete sequences of bacterial genomes, or various organism chromosome sequences. Jurassic Park Treasury (talk) 03:05, August 2, 2013 (UTC) :I think that there is still something wrong with the order of the nucleotides. What do you get what you put it in reversed order? BastionMonk (talk) 09:02, August 2, 2013 (UTC) This was the result when I got the antisense actin DNA code: CGGCCGAAGCGGCCGCTACTACGGGGGTCT Jurassic Park Treasury (talk) 00:04, August 3, 2013 (UTC) When I put it in the reverse option instead of the complementary option, I got the same results as the original code when I BLASTed it (mRNA sequences). Jurassic Park Treasury (talk) 01:57, August 4, 2013 (UTC) So, what do you think is wrong with the order of the nucleotides? Jurassic Park Treasury (talk) 11:43, August 4, 2013 (UTC) :Well, I got problems too when I tried it. So, used the Histone 4 code instead. This is what the code should look like: protein: D A V T Y T E H A K mRNA: GATGCCGTGACCTACACCGAGCACGCCAAG gene: CTACGGCACTGGATGTGGCTCGTGCGGTTC If I BLAST the gene code I only get mRNA's and other stuff. So, I used the mRNA code and restricted the search for Galliformes (Chickens). I got matches with Histone 4 genes. However, I got mRNA's too. Very very odd. BastionMonk (talk) 22:00, August 4, 2013 (UTC) This opens up a lot of questions. Is it really possible to deduce the gene code from protein code afterall? Do we need to consult an experienced biologist about this? I'm starting to wonder. Jurassic Park Treasury (talk) 02:51, August 5, 2013 (UTC) I'm almost certainly overreacting about the first question, but maybe we do need help from a more experienced biologist. Jurassic Park Treasury (talk) 05:48, August 5, 2013 (UTC) :Dude, you CAN deduce the gene code from protein code. No doubt about that. This is the central dogma of biology. There are a 1000 reasons why BLAST comes up with other things than Histone4 genes. These sequences are VERY short and very ancient, they appear in a wide range of genes. :I think we have more succes if the 3th nucleotide in each codon is an N than that the software just choses a nucleotide. The engine that claims to use data from chickens isn't working. Chickens Histone4 gene only had a lose correlation with the dino gene. However, when I saw the alignments, the only thing that differed where the 3th positions in the codons. So, the translator doesn't fill this gap with chicken data. Unless the translator knows beforehand what protein it is, it can't know. BastionMonk (talk) 09:39, August 5, 2013 (UTC) :I used the other translator: protein: D A V T Y T E H A K mRNA: GAYGCNGTNACNTAYACNGARCAYGCNAAR gene: CTRCGNCANTGNATRTGNCTYGTRCGNTTY Then I searched for the Chicken Histone 4 gene in GenBank. I first encountered the mRNA script of the gene, so I used that. I made an alignment, and this was what I got: This is a 100% match, except for the 3th positions in the codon which we can't know. I don't know why gene code is so hard to find in GenBank. However, that is what causes our problems. This is the correct way to translate protein to DNA. BastionMonk (talk) 10:16, August 5, 2013 (UTC) So, we have to use the ambigious nucleotides again? That sucks. Jurassic Park Treasury (talk) 03:40, August 6, 2013 (UTC) :Well, BLAST can't handle non-nucleotide letters. So, we could still use the chicken-inspired translator, but it won't help getting better matches with chickens. After we know what kind of gene we're dealing with, we can create alignments between the dino and bird genes. After that, we could fill in the 3th codon positions with the nucleotides in the chicken genes. BastionMonk (talk) 08:50, August 6, 2013 (UTC) Before we could fill in the codons, we would also have to look at the genes of other birds and reptiles, and deduce what the dinosaur codons were. Also, for some genes like COL1A1, there seem to be no chicken DNA sequences on GenBank. Jurassic Park Treasury (talk) 23:35, August 6, 2013 (UTC) :We don't know that for sure. In most cases GenBank stores DNA or RNA fragments. Sometimes these fragments are entire chromosomes. I think they're still in the process of chopping the entire chromosomes into individuals regions and genes. I also didn't got a gene hit for Histone4, while I did got a mRNA hit for that. BastionMonk (talk) 07:25, August 7, 2013 (UTC) Here's the gene code. Jurassic Park Treasury (talk) 07:33, August 7, 2013 (UTC) :Thanks! I don't know about your PC, but when I enter "Chicken histone H4 protein gene", the gene I want is on the second page. Therefore, I changed my search terms and found mRNA's in the end. BastionMonk (talk) 13:20, August 7, 2013 (UTC) It turns out that all DNA sequences stored in ncbi are sense-DNA. It sequence is therefore identical to mRNA's (with U changed for T of course). I think that solves the issue. Now that I had the gene sequence, I aligned the gene and the mRNA using Spidey: Genomic sequence: M74534.1 mRNA sequence(s): NM_001037843 It was then that I saw that the sequences are identical. I somehow remembered that the antisense strand is the reference sequence and therefore the one featured in all documentation. However, it turns out it is sense-DNA. BastionMonk (talk) 14:29, August 7, 2013 (UTC) All of them? I find that a bit hard to believe. Are you sure it's not just the histone H4 that's in sense format? This is supposed to be the entire enamelin gene in mice, yet this is supposed to be the complete mRNA code in the same species. Note how the latter is a lot longer. Yet again, this is also an enamelin mRNA sequence, yet it's bigger than the other mRNA. Jurassic Park Treasury (talk) 01:36, August 8, 2013 (UTC) This is what you should do: * Go to Spidey * Fill in: * Genomic sequence: AF303737.1 * mRNA sequence(s): U82698.1 and NM_017468.3 * Click "Align" Here you will see that those mRNA's align with the genomic sequence. The mRNA consists of 10 s. Only Exon 3-10 code for protein. The latter mRNA aligns 100%. Could that be an update of the previous? BastionMonk (talk) 09:24, August 8, 2013 (UTC) I don't quite understand. I know the sense DNA aligns perfectly with the mRNA, but why is the DNA gene much longer than the mRNA gene? My best guess is that the DNA gene contains a lot of introns. Jurassic Park Treasury (talk) 10:12, August 8, 2013 (UTC) Replacing the third nucleotide of every codon in our dinosaur genes with an ambiguous nucleotide sounds like a bit of a long job. Here, I've done it with the T. rex ''collagen type |, alpha 2 gene. CCNGANGGNCCNCTNTCNCCNCGNCANCCNGGNCGNCCNGGNTANCCNTCNTCN This is all starting to get VERY confusing for me. Jurassic Park Treasury (talk) 06:53, August 20, 2013 (UTC) :What do you mean? If you use the right '''protein' -> DNA translator it will automatically put an N (or something else) at the third position. Did you do it by hand? BastionMonk (talk) 09:14, August 20, 2013 (UTC) I did it by hand. Jurassic Park Treasury (talk) 21:39, August 23, 2013 (UTC) I did the tyrannosaur COL1A1 gene by hand now. CCNCGNTGNCCNCGNGGNCCNTANCGNCCNCGNGGNCCNAANGGNCCNCGNTCNCCNCGNGGNCCNGGNGTNCCNGGNTCNCCNCGNGGNCCNGGNT TNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCNCANGTN CCNGGNGGNCCNGGNGTNCCNGGNTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCNTCNCGNCCNGGNGGNCCNCGNTGNCCNAANGGNCCNCGNCGNCCNTCN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCNCANCANCCNGANGGNCCNGTNTCN Also, I'm starting to get a bit worried that there might not be many bird or reptile antisense DNA sequences on the various online databases to compare our antisense DNA to. Jurassic Park Treasury (talk) 02:51, August 26, 2013 (UTC) Sense and antisense Since the complementary translator cannot translate non-nucleotide letters, I had to change an ambiguous sense sequence (T. rex COL1A2) into the antisense sequence by hand. Would this be a correct translation? *Sense: GGNYTNCCNGGNGARWSNGGNGCNGTNGGNCCNGCNGGNCCNATHGGNWSNMGNTRR *Anti: CCNRANGGNCCNCTYSWNCCNCGNCANCCNGGNCGNCCNGGNTAGCCNSWNKCNAYY Jurassic Park Treasury (talk) 03:05, August 30, 2013 (UTC) When translating an ambiguous sense sequence into an ambiguous antisense sequence, would it be safe to translate all Hs into Gs, since H means all nucleotides except for G? Or would it be safer to turn the H into a D, which means all except C? Jurassic Park Treasury (talk) 04:31, September 5, 2013 (UTC) Aligning amino acid sequences with nucleotide sequences This page has the protein and DNA code for the peregrine falcon COL1A1 gene. In the case of the amino acid sequence, here is an aligment between one region of the T. rex sequence and the falcon sequence. *Tyrannosaur: GATGAPGIAGAPGFPGARGAPGPQGPSGAPGPK *Falcon: GATGAPGIAGAPGFPGARGPSGPQGPSGAPGPK They are only two amino acids different from each other. However, which region of the DNA sequence is the falcon GATGAPGIAGAPGFPGARGPSGPQGPSGAPGPK coded by? Is there a program which allows you to align an amino acid sequence and a DNA sequence? Jurassic Park Treasury (talk) 01:46, October 1, 2013 (UTC) Bastion, if there isn't a program for that, then would you mind aligning the falcon collagen amino acid sequence with the DNA sequence to see which set of nucleotides codes for each of the amino acids? It will help us fill in the gaps. Jurassic Park Treasury (talk) 05:34, October 18, 2013 (UTC) Never mind that. Apart from two amino acids, the T. rex sequence was identical to the falcon sequence, meaning I only had to change two amino acids. So, I just changed the two amino acids in the falcon sequence to those in the rex sequence (rex amino acids in lower case). MFSFVDSRLLLLIAATVLLTRGQGEEDIQTGSCIQDGLTYNDKDVWKPEPCQICVCDSGN ILCDEVICEDTSDCPNAEIPFGECCPICPDTDASPVYPESAGVEGPKGDTGPKGDRGLPG PPGRDGIPGQPGLPGPPGPPGPPGLGGNFAPQMSYGYDEKAGGMAVPGPMGPAGPRGLPG PPGAPGPQGFQGPPGEPGEPGASGPMGPRGPAGPPGKNGDDGEAGKPGRPGERGPPGPQG ARGLPGTAGLPGMKGHRGFSGLDGAKGEPGPAGPKGEPGSPGENGAPGQMGPRGLPGERG RPGPSGPAGARGNDGAPGAAGPPGPTGPAGPPGFPGAAGAKGETGPQGARGSEGPQGARG EPGPPGPAGAAGPAGNPGADGQPGAKGATGAPGIAGAPGFPGAR'Gap'GPQGPSGAPGPKG NSGEPGAPGNKGDTGAKGEPGPAGVQGPPGPAGEEGKRGARGEPGPAGLPGPAGERGAPG SRGFPGADGIAGPKGPPGERGSPGPAGPKGSPGEAGRPGEPGLPGAKGLTGSPGSPGPDG KTGPPGPAGQDGRPGPPGPPGARGQAGVMGFPGPKGAAGEPGKPGERGAPGPPGAVGAAG KDGEAGAQGPPGPTGPAGERGEQGPAGAPGFQGLPGPAGPPGEAGKPGEQGVPGDAGAPG PAGARGERGFPGERGVQGPPGPQGPRGANGAPGNDGAKGDAGAPGAPGNQGPPGLQGMPG ERGAAGLPGAKGDRGDPGPKGADGAPGKDGLRGLTGPIGPPGPAGAPGDKGEAGPPGPAG PTGARGAPGDRGEPGPPGPAGFAGPPGADGQPGAKGETGDAGAKGDAGPPGPAGPTGAPG PAGAVGAPGPKGARGSAGPPGATGFPGAAGRVGPPGPSGNIGLPGPPGPSGKEGGKGPRG ETGPAGRPGEPGPAGPPGPPGEKGSPGADGPIGAPGTPGPQGIAGQRGVVGLPGQRGERG FPGLPGPSGEPGKQGPSGSPGERGPPGPMGPPGLAGPPGEAGREGAPGAEGAPGRDGAAG PKGDRGETGPAGPPGAPGAPGAPGPVGPAGKNGDRGETGPQGPAGPPGPAGARGPAGPQG PRGDKGETGEQGDRGMKGHRGFSGLQGPPGPPGSPGEQGPSGASGPAGPRGPPGSAGAAG KDGLNGLPGPIGPPGPRGRTGDVGPVGPPGPPGPPGPPGPPSGGFDFSFLPQPPQEKAHD GGRYYRADDANVMRDRDLEVDTTLKSLSQQIENIRSPEGTRKNPARTCRDLKMCHGDCKS GEYWIDPNQGCNLDAIKVYCNMETGETCVYPTQATIAQKNWYLSKNPKEKKHIWFGETMS DGFQFEYGGEGSNPADVAIQLTFLRLMSTEATQNITYHCKNSVAYMDHDTGNLKKALLLQ GANEIEIRAEGNSRFTYGVTEDGCTSHTGAWGKTVIEYKTTKTSRLPIIDLAPMDVGAPD QEFGIDIGPVCFL So, as always, I used the translator. ATGTTYWSNTTYGTNGAYWSNMGNYTNYTNYTNYTNATHGCNGCNACNGTNYTNYTNACN MGNGGNCARGGNGARGARGAYATHCARACNGGNWSNTGYATHCARGAYGGNYTNACNTAY AAYGAYAARGAYGTNTGGAARCCNGARCCNTGYCARATHTGYGTNTGYGAYWSNGGNAAY ATHYTNTGYGAYGARGTNATHTGYGARGAYACNWSNGAYTGYCCNAAYGCNGARATHCCN TTYGGNGARTGYTGYCCNATHTGYCCNGAYACNGAYGCNWSNCCNGTNTAYCCNGARWSN GCNGGNGTNGARGGNCCNAARGGNGAYACNGGNCCNAARGGNGAYMGNGGNYTNCCNGGN CCNCCNGGNMGNGAYGGNATHCCNGGNCARCCNGGNYTNCCNGGNCCNCCNGGNCCNCCN GGNCCNCCNGGNYTNGGNGGNAAYTTYGCNCCNCARATGWSNTAYGGNTAYGAYGARAAR GCNGGNGGNATGGCNGTNCCNGGNCCNATGGGNCCNGCNGGNCCNMGNGGNYTNCCNGGN CCNCCNGGNGCNCCNGGNCCNCARGGNTTYCARGGNCCNCCNGGNGARCCNGGNGARCCN GGNGCNWSNGGNCCNATGGGNCCNMGNGGNCCNGCNGGNCCNCCNGGNAARAAYGGNGAY GAYGGNGARGCNGGNAARCCNGGNMGNCCNGGNGARMGNGGNCCNCCNGGNCCNCARGGN GCNMGNGGNYTNCCNGGNACNGCNGGNYTNCCNGGNATGAARGGNCAYMGNGGNTTYWSN GGNYTNGAYGGNGCNAARGGNGARCCNGGNCCNGCNGGNCCNAARGGNGARCCNGGNWSN CCNGGNGARAAYGGNGCNCCNGGNCARATGGGNCCNMGNGGNYTNCCNGGNGARMGNGGN MGNCCNGGNCCNWSNGGNCCNGCNGGNGCNMGNGGNAAYGAYGGNGCNCCNGGNGCNGCN GGNCCNCCNGGNCCNACNGGNCCNGCNGGNCCNCCNGGNTTYCCNGGNGCNGCNGGNGCN AARGGNGARACNGGNCCNCARGGNGCNMGNGGNWSNGARGGNCCNCARGGNGCNMGNGGN GARCCNGGNCCNCCNGGNCCNGCNGGNGCNGCNGGNCCNGCNGGNAAYCCNGGNGCNGAY GGNCARCCNGGNGCNAARGGNGCNACNGGNGCNCCNGGNATHGCNGGNGCNCCNGGNTTY CCNGGNGCNMGNGGNGCNCCNGGNCCNCARGGNCCNWSNGGNGCNCCNGGNCCNAARGGN AAYWSNGGNGARCCNGGNGCNCCNGGNAAYAARGGNGAYACNGGNGCNAARGGNGARCCN GGNCCNGCNGGNGTNCARGGNCCNCCNGGNCCNGCNGGNGARGARGGNAARMGNGGNGCN MGNGGNGARCCNGGNCCNGCNGGNYTNCCNGGNCCNGCNGGNGARMGNGGNGCNCCNGGN WSNMGNGGNTTYCCNGGNGCNGAYGGNATHGCNGGNCCNAARGGNCCNCCNGGNGARMGN GGNWSNCCNGGNCCNGCNGGNCCNAARGGNWSNCCNGGNGARGCNGGNMGNCCNGGNGAR CCNGGNYTNCCNGGNGCNAARGGNYTNACNGGNWSNCCNGGNWSNCCNGGNCCNGAYGGN AARACNGGNCCNCCNGGNCCNGCNGGNCARGAYGGNMGNCCNGGNCCNCCNGGNCCNCCN GGNGCNMGNGGNCARGCNGGNGTNATGGGNTTYCCNGGNCCNAARGGNGCNGCNGGNGAR CCNGGNAARCCNGGNGARMGNGGNGCNCCNGGNCCNCCNGGNGCNGTNGGNGCNGCNGGN AARGAYGGNGARGCNGGNGCNCARGGNCCNCCNGGNCCNACNGGNCCNGCNGGNGARMGN GGNGARCARGGNCCNGCNGGNGCNCCNGGNTTYCARGGNYTNCCNGGNCCNGCNGGNCCN CCNGGNGARGCNGGNAARCCNGGNGARCARGGNGTNCCNGGNGAYGCNGGNGCNCCNGGN CCNGCNGGNGCNMGNGGNGARMGNGGNTTYCCNGGNGARMGNGGNGTNCARGGNCCNCCN GGNCCNCARGGNCCNMGNGGNGCNAAYGGNGCNCCNGGNAAYGAYGGNGCNAARGGNGAY GCNGGNGCNCCNGGNGCNCCNGGNAAYCARGGNCCNCCNGGNYTNCARGGNATGCCNGGN GARMGNGGNGCNGCNGGNYTNCCNGGNGCNAARGGNGAYMGNGGNGAYCCNGGNCCNAAR GGNGCNGAYGGNGCNCCNGGNAARGAYGGNYTNMGNGGNYTNACNGGNCCNATHGGNCCN CCNGGNCCNGCNGGNGCNCCNGGNGAYAARGGNGARGCNGGNCCNCCNGGNCCNGCNGGN CCNACNGGNGCNMGNGGNGCNCCNGGNGAYMGNGGNGARCCNGGNCCNCCNGGNCCNGCN GGNTTYGCNGGNCCNCCNGGNGCNGAYGGNCARCCNGGNGCNAARGGNGARACNGGNGAY GCNGGNGCNAARGGNGAYGCNGGNCCNCCNGGNCCNGCNGGNCCNACNGGNGCNCCNGGN CCNGCNGGNGCNGTNGGNGCNCCNGGNCCNAARGGNGCNMGNGGNWSNGCNGGNCCNCCN GGNGCNACNGGNTTYCCNGGNGCNGCNGGNMGNGTNGGNCCNCCNGGNCCNWSNGGNAAY ATHGGNYTNCCNGGNCCNCCNGGNCCNWSNGGNAARGARGGNGGNAARGGNCCNMGNGGN GARACNGGNCCNGCNGGNMGNCCNGGNGARCCNGGNCCNGCNGGNCCNCCNGGNCCNCCN GGNGARAARGGNWSNCCNGGNGCNGAYGGNCCNATHGGNGCNCCNGGNACNCCNGGNCCN CARGGNATHGCNGGNCARMGNGGNGTNGTNGGNYTNCCNGGNCARMGNGGNGARMGNGGN TTYCCNGGNYTNCCNGGNCCNWSNGGNGARCCNGGNAARCARGGNCCNWSNGGNWSNCCN GGNGARMGNGGNCCNCCNGGNCCNATGGGNCCNCCNGGNYTNGCNGGNCCNCCNGGNGAR GCNGGNMGNGARGGNGCNCCNGGNGCNGARGGNGCNCCNGGNMGNGAYGGNGCNGCNGGN CCNAARGGNGAYMGNGGNGARACNGGNCCNGCNGGNCCNCCNGGNGCNCCNGGNGCNCCN GGNGCNCCNGGNCCNGTNGGNCCNGCNGGNAARAAYGGNGAYMGNGGNGARACNGGNCCN CARGGNCCNGCNGGNCCNCCNGGNCCNGCNGGNGCNMGNGGNCCNGCNGGNCCNCARGGN CCNMGNGGNGAYAARGGNGARACNGGNGARCARGGNGAYMGNGGNATGAARGGNCAYMGN GGNTTYWSNGGNYTNCARGGNCCNCCNGGNCCNCCNGGNWSNCCNGGNGARCARGGNCCN WSNGGNGCNWSNGGNCCNGCNGGNCCNMGNGGNCCNCCNGGNWSNGCNGGNGCNGCNGGN AARGAYGGNYTNAAYGGNYTNCCNGGNCCNATHGGNCCNCCNGGNCCNMGNGGNMGNACN GGNGAYGTNGGNCCNGTNGGNCCNCCNGGNCCNCCNGGNCCNCCNGGNCCNCCNGGNCCN CCNWSNGGNGGNTTYGAYTTYWSNTTYYTNCCNCARCCNCCNCARGARAARGCNCAYGAY GGNGGNMGNTAYTAYMGNGCNGAYGAYGCNAAYGTNATGMGNGAYMGNGAYYTNGARGTN GAYACNACNYTNAARWSNYTNWSNCARCARATHGARAAYATHMGNWSNCCNGARGGNACN MGNAARAAYCCNGCNMGNACNTGYMGNGAYYTNAARATGTGYCAYGGNGAYTGYAARWSN GGNGARTAYTGGATHGAYCCNAAYCARGGNTGYAAYYTNGAYGCNATHAARGTNTAYTGY AAYATGGARACNGGNGARACNTGYGTNTAYCCNACNCARGCNACNATHGCNCARAARAAY TGGTAYYTNWSNAARAAYCCNAARGARAARAARCAYATHTGGTTYGGNGARACNATGWSN GAYGGNTTYCARTTYGARTAYGGNGGNGARGGNWSNAAYCCNGCNGAYGTNGCNATHCAR YTNACNTTYYTNMGNYTNATGWSNACNGARGCNACNCARAAYATHACNTAYCAYTGYAAR AAYWSNGTNGCNTAYATGGAYCAYGAYACNGGNAAYYTNAARAARGCNYTNYTNYTNCAR GGNGCNAAYGARATHGARATHMGNGCNGARGGNAAYWSNMGNTTYACNTAYGGNGTNACN GARGAYGGNTGYACNWSNCAYACNGGNGCNTGGGGNAARACNGTNATHGARTAYAARACN ACNAARACNWSNMGNYTNCCNATHATHGAYYTNGCNCCNATGGAYGTNGGNGCNCCNGAY CARGARTTYGGNATHGAYATHGGNCCNGTNTGYTTYYTN So, all you need to do is align the normal falcon nucleotide sequence (too long a task for me) with the above nucleotide sequence, and fill in all the gaps except the two changed codons. To fill that in, we would need to know what the falcon codons for AP are, which either you or I could do by simply looking at the alignment. After completing the gene, I would then translate the finished sense sequence into an antisense sequence. Jurassic Park Treasury (talk) 06:09, October 18, 2013 (UTC) :that was more work than I thought. I used Mobyle Portal. Anyway: T. rex prot: G A R G A P G Falcon prot: G A R G P''' '''S G T. rex DNA?: GG?GC?AG?GG?GC?CC?GG? Falcon DNA: ggtgcccgcggtccctccgga Filled gaps: ggtgcccgcggt'g'''cc'c'ccgga So if if past this back into the rest of the sequence: atgttcagctttgtggattctcggttactgctgttgatagcagcgactgtactactcacc cgcgggcaaggagaagaagacattcaaactggaagctgcatacaggatgggctaacatac aacgacaaggatgtgtggaaacccgaaccctgccagatctgcgtctgcgacagtggcaac atcctctgcgatgaggtgatctgcgaggacacctccgactgccccaatgctgagatcccc ttcggagagtgctgccccatctgtcccgacaccgacgcctcccctgtctacccagaaagc gctggagtagagggccctaagggagacaccggccccaaaggagacaggggactccccggc ccccctggcagagatggcatccctggacagcctggcctcccgggacccccaggccctcca ggtcctccaggccttggcggaaacttcgctcctcaaatgtcttatggctacgatgagaaa gccggtggcatggccgtgcctggccccatgggtccagctggtccccgcggtctccccggt cctcctggtgctcctggtcctcaaggtttccaaggtccccctggtgaacccggagagcct ggtgcatctggtcccatgggtccccgtggtcctgctggcccccctggcaagaatggagat gacggtgaagctggaaagcccggccgtcccggagagcgcggtccacccggcccccagggc gcacgtggtctcccaggaacagccggtctgccaggcatgaagggtcacagaggcttcagt ggtctggatggtgccaagggtgagcctggtcctgctggccccaagggtgagcccggcagc cccggggagaacggtgctcctgggcagatgggtcctcgtgggcttcccggcgagagaggc cgtcctggtccttctggccctgctggtgctcgtggtaacgatggtgctcctggtgctgcc ggtcctcccggtccaactggccccgctggtccccctggcttccctggtgctgctggtgct aagggtgaaaccggtccccagggagctcgtggcagtgaaggtccgcagggtgcccgtggt gagcccggtccccctggccctgctggcgctgctggtcctgctgggaaccccggtgctgat ggtcaacctggtgccaagggtgcaactggtgctcctggcattgctggtgctcctggcttc ccc'ggtgcccgcggtgcccccgga'''ccccagggtcccagcggtgcccccggtcccaagggt aacagcggtgaacccggtgctccaggcaacaagggagacactggtgccaaaggcgaacct ggtcctgctggtgtccaaggtccccccggcccagccggtgaggaaggcaagagaggagct cgtggtgagcctggccctgctggacttcctggccccgctggcgaacgtggtgctcctggc agccgcggcttccctggtgctgatggcattgctggtcccaagggtccccccggcgagcgt ggctcccctggccctgccggccccaaaggatctcctggtgaagctggacgccctggggaa cctggcctccctggtgctaagggtctgactggaagccctgggagccctggtcctgacggc aagactggcccccccggtcccgctggtcaagatggtcgccccggcccccccggcccccct ggtgccagaggtcaagctggtgtgatgggtttccctggtcccaaaggtgctgcgggtgag cctggcaagcccggcgagagaggtgctcccggtccccccggcgccgttggtgctgctggt aaagatggtgaagctggtgcccaaggtcctcccggccccaccggtcctgctggagaaaga ggtgaacaaggtcctgctggtgctcctggcttccagggtctgccgggccctgctggcccc cccggcgaggctggcaagcctggtgaacagggtgtccccggagatgctggtgcccccggt cccgctggtgccaggggtgagagaggtttccccggtgaacgtggtgtccaaggccctccc ggtccccaaggtcctcgtggtgctaacggtgctcccggtaacgatggtgctaagggtgat gctggtgctcccggtgcccccgggaaccaagggccccccggtctgcagggtatgcccgga gagcgtggtgctgctggcctgccaggtgccaagggtgacaggggtgaccccggtcccaaa ggtgctgacggtgctcctggcaaagacggtctccgaggtctgactggtcccatcggcccc cctggccctgctggtgctcccggtgacaagggtgaagctggtcccccgggtcctgctggt cccactggtgcccgtggtgctcctggtgaccgtggcgagcccggccctcctggtcctgct ggatttgctggcccccccggtgccgatggccagcctggtgctaaaggtgaaactggtgat gctggagccaagggtgatgccggtccccccggccctgccggccccactggtgctcctggc cctgctggtgctgttggtgctcctggtcccaaaggtgctcgtggtagtgctggaccccct ggtgctactggtttccctggtgctgctggaagagttggtccccctggcccctctggaaac atcggcctccctggcccccctggccccagcgggaaggaaggtggcaaaggaccccgtggt gaaaccggccccgctgggcgccctggtgaacctggccccgctggcccccctggcccccct ggtgagaagggctctcctggtgccgatggccccattggagctcctggcacccccggaccc caaggtatcgccggccagcgtggtgttgtcggtctccctggacagagaggagaaagaggc ttccctgggctgcctggcccctctggtgaacccggcaagcaaggtccctctggttcccct ggcgagcgcggtcctcccggccccatgggcccccccggcctggcgggaccccccggtgaa gctggacgtgagggtgctcctggtgctgaaggtgcccctggtcgtgatggtgctgctggt cccaagggtgatcgtggtgagactggccctgctggcccccctggtgctcccggtgcccct ggtgcccccggccccgttggtcctgctggcaagaatggagatcgcggtgagaccggtccc caaggtcccgctggcccccctggtcctgctggtgctcgtggtcctgctggtccacaaggt ccccgtggtgacaaaggtgaaactggtgaacagggtgacagaggcatgaaaggtcacaga ggcttctccggtctccagggaccacctggtcctcctggctctcctggtgaacaaggtcct tctggtgcttctggtcccgccggtccaagaggtcctcctggctctgctggtgctgccggc aaagatggtctcaacgggctgcccggccccatcggcccccccggcccccgcggtcgcacc ggtgatgttggccctgtcggtccccctggcccccctggcccccctggtcctcccggcccc cccagcggtggcttcgacttcagcttcctgccccagccaccccaggagaaggcccacgat ggtggacgctactaccgagctgatgatgccaacgtaatgcgcgaccgggacctggaagtt gacaccaccctcaagagcctgagccaacagatcgagaacatccgcagccccgagggcacc cgtaaaaaccctgcccgtacctgccgcgacctgaagatgtgccatggcgattgtaagagc ggcgaatactggatcgaccccaaccaaggctgcaacctggatgccatcaaggtctactgt aacatggagacaggcgagacatgcgtctaccccacccaggccaccattgcccagaagaac tggtacctcagtaagaatcccaaggagaagaagcacatttggtttggcgagacgatgagt gacggcttccagttcgagtatggtggtgagggctccaaccctgctgacgtcgccatccag ctaaccttcctccgcctcatgtccactgaggccacccagaacatcacctaccactgcaag aacagcgtcgcctacatggaccacgacactggcaacctgaagaaggcccttctcctccaa ggagccaacgagatcgagatcagggctgaaggcaatagccgcttcacctacggtgtcacc gaggacggctgcacgagtcacaccggtgcttggggcaagacagtcatcgagtacaagacg acgaagacctcccgcctgcccatcatagatttggctcccatggacgttggtgctccagac caggaattcggcattgacatcggccccgtctgcttcttgtaa Only two nucleotides changed. BastionMonk (talk) 10:39, October 18, 2013 (UTC) Thanks. Jurassic Park Treasury (talk) 11:41, October 18, 2013 (UTC)